fix: Lots of small bugs based on code analysis by claude #16
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The following issues were discovered by Claude and have been resolved:
HASH_FAILprinted under--statusand didn't name the file-c,-o,--legacywere ignoredFAILED-oappended to an existing file-q/-scheck didn't match its messageNew tests exist for some of the issues, and others have been tested extensively by hand. This was done to prepare for the 1.0.0 release and to squash any bugs without changing user-facing APIs